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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.743663346254825,

Latest revision as of 11:24, 17 September 2013


Full id: C506_Smooth_Renal_Endothelial_hepatic_Adipocyte_Fibroblast_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr6:132269835..132269894,-p7@CTGF
Hg19::chr6:132269939..132269966,-p12@CTGF
Hg19::chr6:132270118..132270130,-p13@CTGF
Hg19::chr6:132270276..132270290,-p10@CTGF
Hg19::chr6:132270471..132270530,-p5@CTGF
Hg19::chr6:132270532..132270550,-p9@CTGF
Hg19::chr6:132270563..132270604,-p3@CTGF
Hg19::chr6:132270672..132270706,-p8@CTGF
Hg19::chr6:132271115..132271160,-p@chr6:132271115..132271160
-
Hg19::chr6:132271128..132271174,+p@chr6:132271128..132271174
+
Hg19::chr6:132271161..132271207,-p@chr6:132271161..132271207
-
Hg19::chr6:132271279..132271304,-p@chr6:132271279..132271304
-
Hg19::chr6:132271546..132271561,-p@chr6:132271546..132271561
-
Hg19::chr6:132271569..132271590,-p@chr6:132271569..132271590
-
Hg19::chr6:132271627..132271658,-p@chr6:132271627..132271658
-
Hg19::chr6:132271932..132271967,-p6@CTGF
Hg19::chr6:132271980..132271991,-p16@CTGF
Hg19::chr6:132271998..132272086,-p2@CTGF
Hg19::chr6:132272504..132272519,-p1@CTGF


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
vasculature1.21e-3278
vascular system1.21e-3278
vessel5.01e-2868
splanchnic layer of lateral plate mesoderm1.99e-2783
epithelial tube1.48e-26117
cardiovascular system3.07e-26109
circulatory system7.70e-26112
epithelial tube open at both ends5.57e-2559
blood vessel5.57e-2559
blood vasculature5.57e-2559
vascular cord5.57e-2559
artery3.52e-2242
arterial blood vessel3.52e-2242
arterial system3.52e-2242
unilaminar epithelium6.40e-20148
systemic artery4.66e-1733
systemic arterial system4.66e-1733
trunk mesenchyme1.01e-16122
epithelial vesicle8.39e-1678
muscle tissue1.04e-1564
musculature1.04e-1564
musculature of body1.04e-1564
skeletal muscle tissue1.70e-1562
striated muscle tissue1.70e-1562
myotome1.70e-1562
mesenchyme3.13e-14160
entire embryonic mesenchyme3.13e-14160
dense mesenchyme tissue1.07e-1373
somite1.26e-1371
presomitic mesoderm1.26e-1371
presumptive segmental plate1.26e-1371
dermomyotome1.26e-1371
trunk paraxial mesoderm1.26e-1371
paraxial mesoderm3.77e-1372
presumptive paraxial mesoderm3.77e-1372
trunk6.37e-13199
aorta5.44e-1221
aortic system5.44e-1221
organism subdivision1.32e-11264
squamous epithelium9.88e-1125
multilaminar epithelium1.01e-1083
simple squamous epithelium1.69e-1022
mesoderm3.27e-10315
mesoderm-derived structure3.27e-10315
presumptive mesoderm3.27e-10315
anatomical cluster3.50e-10373
cell layer6.17e-10309
anatomical conduit7.30e-10240
epithelium1.51e-09306
blood vessel endothelium3.01e-0918
endothelium3.01e-0918
cardiovascular system endothelium3.01e-0918
tube1.74e-08192
multi-cellular organism1.77e-07656
heart3.17e-0724
primitive heart tube3.17e-0724
primary heart field3.17e-0724
anterior lateral plate mesoderm3.17e-0724
heart tube3.17e-0724
heart primordium3.17e-0724
cardiac mesoderm3.17e-0724
cardiogenic plate3.17e-0724
heart rudiment3.17e-0724
smooth muscle tissue6.23e-0715
primary circulatory organ9.14e-0727


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.11206
MA0004.10.563888
MA0006.10.0925234
MA0007.11.61489
MA0009.10.580032
MA0014.10.0234339
MA0017.10.741662
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.10.269828
MA0040.10.507819
MA0041.10.206566
MA0042.12.32519
MA0043.10.580321
MA0046.10.570066
MA0048.11.36881
MA0050.10.542713
MA0051.10.266537
MA0052.11.27353
MA0055.11.15636
MA0056.10
MA0057.10.00844127
MA0058.10.12994
MA0059.10.129144
MA0060.10.0387582
MA0061.10.290613
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.10.0187693
MA0069.10.566544
MA0070.10.556335
MA0071.10.674412
MA0072.10.552241
MA0073.10.0285812
MA0074.10.265952
MA0076.10.139892
MA0077.10.545231
MA0078.10.915792
MA0081.11.30972
MA0083.12.44546
MA0084.11.06048
MA0087.10.550016
MA0088.10.0542435
MA0089.10
MA0090.10.891785
MA0091.10.195166
MA0092.10.168981
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.12.15263
MA0101.10.0959778
MA0103.10.0875643
MA0105.10.035705
MA0106.10.302526
MA0107.10.0591705
MA0108.20.432749
MA0109.10
MA0111.11.48573
MA0113.10.847356
MA0114.10.0569149
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.13.91907
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.11.47785
MA0136.10.27535
MA0139.11.57231
MA0140.10.238066
MA0141.10.801079
MA0142.10.407878
MA0143.10.315941
MA0144.10.0508083
MA0145.10.675341
MA0146.10.00163852
MA0147.10.838322
MA0148.10.606512
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.20.000254038
MA0138.20.347473
MA0002.20.589508
MA0137.20.105044
MA0104.20.980761
MA0047.20.292798
MA0112.21.88162
MA0065.20.0221473
MA0150.10.145358
MA0151.10
MA0152.11.26389
MA0153.10.67139
MA0154.10.100086
MA0155.10.593063
MA0156.10.106343
MA0157.10.384449
MA0158.10
MA0159.12.33438
MA0160.10.222325
MA0161.10
MA0162.10.00688807
MA0163.10.00296327
MA0164.10.32594
MA0080.20.31321
MA0018.20.30364
MA0099.20.681929
MA0079.21.57211e-05
MA0102.21.09681
MA0258.12.04877
MA0259.10.869556
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#10664123.38542507773162.39602138640007e-050.000522308657011557
GATA3#262568.601005165433484.38557728836884e-050.000777764147427328
HEY1#23462194.040111043105713.00127317794054e-123.98791309708564e-10
JUN#372574.60998970243970.0004418850707130040.00411612869248978
JUND#3727165.890243319470341.90674971775736e-112.29422849968734e-09
NR3C1#290875.516377016747960.000145422501243130.00187967581773901
POLR2A#5430192.147453176558074.9316078952508e-072.31380142395372e-05
POU5F1#5460352.96408443977462.46415883246597e-050.00053404084727934
RAD21#5885105.450017839713862.85321341547804e-069.81511053686135e-05
STAT3#677463.321936314890810.006719751575040510.0285622943610621
TAF7#68791810.83132890992791.55076047024434e-183.52853753272002e-16
USF2#739274.786599036604590.0003509309921958220.00353261512230742



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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